Variant report

Variant	rs7133131
Chromosome Location	chr12:21594983-21594984
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21590817..21593579-chr12:21593991..21595948,2	MCF-7	breast:
2	chr12:21589203..21592796-chr12:21593700..21598591,5	MCF-7	breast:
3	chr12:21594525..21596330-chr12:21596660..21599628,2	K562	blood:
4	chr12:21489978..21491916-chr12:21593209..21595561,2	K562	blood:

Variant related genes	Relation type
ENSG00000121350	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1024734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046040	0.84[ASN][1000 genomes]
rs11046044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611002	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11835956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12422251	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12423173	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12423381	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423536	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12424852	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12426100	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12426103	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12817513	0.83[ASN][1000 genomes]
rs12818516	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12826040	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1860948	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110164	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2417987	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4539382	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4762826	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6487224	0.92[CEU][hapmap];0.93[YRI][hapmap]
rs7131809	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7138089	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310391	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs738027	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957415	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7959893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971245	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7973116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974260	0.87[CEU][hapmap]
rs7974817	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9668302	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7133131	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs7133131	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs7133131	IAPP	cis	uninvolved skin	skin_eQTL
rs7133131	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs7133131	PYROXD1	cis	Esophagus Muscularis	GTEx
rs7133131	FLJ22028	cis	normal skin	skin_eQTL
rs7133131	LOC642732	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21591400-21595400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:21591400-21602800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:21591600-21598600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:21591600-21599600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:21591600-21609000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:21591600-21609000	Weak transcription	Brain Angular Gyrus	brain
7	chr12:21591600-21609200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:21591800-21595000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:21591800-21595000	Weak transcription	Fetal Brain Female	brain
10	chr12:21591800-21598600	Weak transcription	Fetal Brain Male	brain
11	chr12:21591800-21599000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:21591800-21600000	Weak transcription	HSMM	muscle
13	chr12:21591800-21601000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:21591800-21609000	Weak transcription	Fetal Heart	heart
15	chr12:21591800-21611000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:21591800-21614600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:21591800-21614800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:21591800-21621000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:21591800-21624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:21592000-21597800	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:21592000-21614200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:21592000-21620600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:21592000-21631000	Weak transcription	Psoas Muscle	Psoas
24	chr12:21592200-21595000	Weak transcription	Stomach Mucosa	stomach
25	chr12:21592200-21595000	Weak transcription	HSMMtube	muscle
26	chr12:21592200-21596600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:21592200-21598400	Weak transcription	Fetal Kidney	kidney
28	chr12:21592200-21598600	Weak transcription	HUVEC	blood vessel
29	chr12:21592200-21609000	Weak transcription	NH-A	brain
30	chr12:21592200-21609000	Weak transcription	NHDF-Ad	bronchial
31	chr12:21592200-21609200	Weak transcription	Brain Substantia Nigra	brain
32	chr12:21592400-21596200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:21592400-21610400	Weak transcription	NHEK	skin
34	chr12:21592600-21595000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:21592600-21595000	Weak transcription	A549	lung
36	chr12:21592600-21609200	Weak transcription	Small Intestine	intestine
37	chr12:21592800-21631400	Weak transcription	K562	blood
38	chr12:21593400-21595400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:21593400-21595600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:21593400-21595800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr12:21593400-21595800	Strong transcription	Primary T cells from cord blood	blood
42	chr12:21593400-21595800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:21593400-21597200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr12:21593400-21604400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:21593400-21606600	Strong transcription	Liver	Liver
46	chr12:21593400-21609000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:21593400-21609000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:21593400-21617800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr12:21593600-21595800	Strong transcription	HepG2	liver
50	chr12:21593600-21596000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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